I've done it! It took me a few days of trial and error, but I officially have a working product. There's not a GUI yet, but I have put together a bash file to automatically assemble the CIA files from CHD files. As a test, I've created working CIAs for both Crash Bandicoot and Um Jammer Lammy; both of which work flawlessly. There are some strange bugs (certain title IDs seem to cause saves to be placed in the wrong location), but overall I haven't seen any glaring issues. I don't know how long it'll take to create a GUI for it, as I'm not very experienced in that department.
Until I've made the GUI, if anybody wants the Crash Bandicoot or Um Jammer Lammy CIAs I've created, let me know!
Also, Merry Christmas everyone!